I love the foundry, but I think it could be imporved. Here are some suggestions I thought of while making missions.
Missions that allow you to have just 2 people (you and an officer)
3-person ground squads (for such missions)
Mulitple Storyline trees, triggered by dialouge choices
Dreadnaught Squadrons (just one dreadnaught, no matter the number of players)
Choose what weapons costumes hold (For the federation, who's only ally is themselves. This make re-skinning troublesome.)
A setting to make friendly NPCs not "die" just be "Disabled" (Like the Zdenia in the last reman mission)
Freindly and enemy squadrons that fight with just their hands, for specific storylines
Skin color that matches the race for costumes,
Please comment, and I'll add more as I think of them.